what is "Console.exe"?
Is the security warning the System File protection dialog?
instead of changing or modifying the cmd.exe file in System32, try renaming & replacing the one in system32\dllcache
Then, if you delete the actual Cmd.exe in system32, windows will show the SFC prompt- allow it to replace the file (unless it asks for your Windows CD, then hit cancel).
If SFC doesn't ask for a CD, then it probably replaced the cmd.exe file with the renamed console.exe, otherwise you should be able to simply copy the one from dllcache to System32.